Europe’s largest population of wild red deer (Cervus elaphus) resides in the British Isles and has been present since the end of the last ice age, c. 11,000BP. Since the mid-19th century, multiple introductions of Japanese sika (Cervus nippon) and wapiti (Cervus canadensis) have taken place across the British Isles. While wapiti introductions have generally gone extinct, sika have thrived and expanded and now often live in sympatry with red deer. Hybridisation between these species has been demonstrated in captivity and in the wild. This study sought to determine the extent of hybridisation and introgression between red and sika across large parts of the British Isles and elucidate some of its potential consequences. Chapter 2 addresses the extent of hybridisation and introgression across Scotland and NW England. A total of 2984 samples from the North Highlands, the central Highlands, the Hebrides, Kintyre and the English Lake District were genotyped at 22 microsatellite loci, which are highly diagnostic for red and sika and strongly diagnostic for red and wapiti and a mitochondrial marker that is diagnostic for red and sika, alongside 49 wapiti samples from Canada. Microsatellite data was analysed using the Bayesian clustering program Structure 2.3 to determine the extent of admixture between species. There was some evidence for very low-level introgression by wapiti into a small number of Scottish red deer (<0.2% of total). Only two areas (both in Kintyre, Argyll) showed extensive introgression with collapse of assortative mating between red and sika (50.4% and 61.8% of sampled individuals were hybrid in West Loch Awe and South Kintyre, respectively). However, rare and widely scattered individuals with low-level sika introgression or cytonuclear disequilibrium suggest hybridisation has occurred in several other places in mainland Scotland and Cumbria in the past without subsequent loss of assortative mating. Chapter 3 addresses the extent of hybridisation in Ireland. There are now an estimated 4,000 red deer in Ireland and their numbers are increasing. It has recently been determined that the red deer in Killarney, County Kerry are descended from an ancient (c. 5,000BP) introduction and therefore merit genetic conservation. Introduction of exotic species, including Japanese sika and North America wapiti, since the 19th century have primarily occurred via the now defunct Powerscourt Park, County Wicklow, which was the source of many translocations to the rest of Ireland as well as to the UK. 374 deer samples from across Ireland were analysed as in Chapter 2. Wapiti introgression was again very low, with trace amounts of introgression detected in a small proportion of samples (0.53%), whilst 41% of 197 deer sampled in Co. Wicklow and 47% of 15 deer sampled in Co. Cork were red-sika hybrids according to either their nuclear genome or mitochondrial haplotype. No pure red deer were detected in Co. Wicklow, suggesting that in this region the red deer has disappeared following hybridisation. Whilst no hybrids were detected among 37 red samples and 77 sika samples in Co. Kerry, the Co. Cork hybrids pose a threat to the Killarney populations due to their proximity. Chapter 4 investigates population genetic structure within red and sika populations across the British Isles and investigates whether low-level introgression by the other species influences the resolved population structure. Structure analysis was conducted separately using 2307 ‘pure’ red deer individuals and 752 ‘pure’ sika animals from the British Isles (defined as Q > 0.95 for red and Q < 0.05 for sika) and then on reduced sample sizes using more stringent purity criteria (Q ≥ 0.99 and Q ≤ 0.01). As might be predicted, the more stringent criteria removed individuals in areas known to contain advanced backcrosses. In red deer, there was some evidence for a loss of within-species population structure under the more stringent criteria, while for sika there was not. Datasets were also analysed using Discriminate Analysis of Principal Components; a multivariate method designed to infer and describe genetic population structure. In red deer, both analytical approaches confirmed the strong separation of the deer on Harris and Lewis from others, and there is support for clusters typified by the other Hebridean islands, Kintyre, central and North Scotland and the English sites. Among sika, both approaches supported the likelihood of three clusters which are presumably the result of bottleneck events as each introduction was made. Chapter 5 investigates the phenotypic consequences of hybridisation by three approaches. Firstly, carcass weight was regressed against genetically-determined hybrid scores (at two stringency levels, see Chapter 4) and heterozygosity (in terms of red and sika alleles). Among hybrids, carcass weight is linearly related to hybrid score (Q) and there is some evidence for a positive relationship with heterozygosity. This suggests that additive genetic variation explains variation in carcass weight to a greater extent than heterosis. Secondly, analysis of five case studies representing individual putative hybrids submitted by stalkers from areas without known hybridisation, two proved to be hybrids, while the other three were pure sika. Lastly, in regions known to contain hybrids, the accuracy of ranger-assigned phenotype averaged 78% and revealed that in Scotland accuracy tends to decline as an individual becomes more genetically intermediate; whilst in Co. Wicklow it is the identification of pure parental animals that is more challenging. In conclusion, the existence of rare and widely scattered advanced red-sika backcrosses with low-level nuclear introgression and/or mitochondrial introgression (e.g. in North of Scotland, Cumbria) highlight that some hybridisation events are followed by extensive backcrossing without the breakdown of assortative mating, while others are followed by the generation of a hybrid swarm (e.g. in South Kintyre, West Loch Awe, Co. Wicklow, Co. Cork). Phenotypic traits can become intermediate due to hybridisation and this may facilitate further gene flow and hybridisation. New molecular tools including next generation sequencing (NGS) will enable better understanding the hybridisation process and its phenotypic consequences in this and other systems.

Anthracnose, caused by <i>Colletotrichum truncatum</i>, is a major disease of lentil (<i>Lens culinaris</i> Medik.) on the Canadian prairies. Resistance to the more virulent race Ct0 of the pathogen is extremely rare within the <i>L. culinaris</i> gene pool thus resistance is being introgressed from <i>Lens ervoides</i>. The overall hypothesis of this project was that resistance derived from <i>Lens ervoides</i> accession L-01-827A would provide uniquely low levels of resistance to <i>Colletotrichum truncatum</i>. Individual studies were performed to: i) test field-resistance of interspecific lines; ii) develop a cutting-method to generate replicated phenotypic data on single plants; iii) study the deterioration of resistance between the juvenile phase (JP) and adult phases (AP) in the line CDC Redberry; and iv) examine genetic control of resistance in a susceptible and partially resistant background. Field evaluations of <i>L. culinaris x L. ervoides</i> lines indicated resistance genes from the wild species will provide unprecedented levels of disease control and heritability of the trait was estimated to be moderate. Single plant phenotyping of resistance is unreliable, thus the feasibility of using clonal propagation of individual plants to generate replicated ratings was evaluated. Results showed consistency in segregation ratios between cutting and seedling-derived plants of the same population, thus the method was utilized for testing of genetic control of segregating populations. CDC Redberry showed varying disease levels depending on the age of the plants with resistance acquisition in the JP that decreased as the plants proceeded through the AP. The F₁, F₂ and F_2:3 generations of two introgression populations were tested for resistance. Resistance from <i>L. ervoides</i> to both races of <i>C. truncatum</i> appeared to be due to the same gene(s) or from the same linkage block in both populations. Models for genetic control were consistent between F₂ and F_2:3 generations, however were different between the populations depending on whether the interspecific line was crossed into a susceptible or partially resistant <i>L. culinaris</i> background. However duplicate recessive epistasis seemed to control susceptibility in the susceptible background and when JP resistance was not a factor. There were significant differences between the JP and AP on more than a third of the F₂s tested supporting different resistance gene action based on growth phase. Resistance in the JP seemed to be due to dominant and recessive epistasis. It was postulated that the the populations may have had segregation distortion commonly found in interspecific populations, thus the previously described genotypes for cotyledon colour and albino plants were used to test the hypothesis of segregation distortion. Segregation of these traits were found to be similarly distorted to previously reported interspecific <i>L. culinaris x L. ervoides</i> populations supporting the hypothesis that continued segregation distortion was found in the introgression populations. Overall, it was found that resistance derived from <i>L. ervoides</i> accession L-01-827A is a highly effective source for the lentil breeding program, however the result suggest more than one backcross to <i>L. culinaris</i> be necessary to properly integrate the resistance genes to eventually obtain fully fertile, adapted lentil cultivars.

Anthracnose, caused by <i>Colletotrichum truncatum</i>, is a major disease of lentil (<i>Lens culinaris</i> Medik.) on the Canadian prairies. Resistance to the more virulent race Ct0 of the pathogen is extremely rare within the <i>L. culinaris</i> gene pool thus resistance is being introgressed from <i>Lens ervoides</i>. The overall hypothesis of this project was that resistance derived from <i>Lens ervoides</i> accession L-01-827A would provide uniquely low levels of resistance to <i>Colletotrichum truncatum</i>. Individual studies were performed to: i) test field-resistance of interspecific lines; ii) develop a cutting-method to generate replicated phenotypic data on single plants; iii) study the deterioration of resistance between the juvenile phase (JP) and adult phases (AP) in the line CDC Redberry; and iv) examine genetic control of resistance in a susceptible and partially resistant background. Field evaluations of <i>L. culinaris x L. ervoides</i> lines indicated resistance genes from the wild species will provide unprecedented levels of disease control and heritability of the trait was estimated to be moderate. Single plant phenotyping of resistance is unreliable, thus the feasibility of using clonal propagation of individual plants to generate replicated ratings was evaluated. Results showed consistency in segregation ratios between cutting and seedling-derived plants of the same population, thus the method was utilized for testing of genetic control of segregating populations. CDC Redberry showed varying disease levels depending on the age of the plants with resistance acquisition in the JP that decreased as the plants proceeded through the AP. The F₁, F₂ and F_2:3 generations of two introgression populations were tested for resistance. Resistance from <i>L. ervoides</i> to both races of <i>C. truncatum</i> appeared to be due to the same gene(s) or from the same linkage block in both populations. Models for genetic control were consistent between F₂ and F_2:3 generations, however were different between the populations depending on whether the interspecific line was crossed into a susceptible or partially resistant <i>L. culinaris</i> background. However duplicate recessive epistasis seemed to control susceptibility in the susceptible background and when JP resistance was not a factor. There were significant differences between the JP and AP on more than a third of the F₂s tested supporting different resistance gene action based on growth phase. Resistance in the JP seemed to be due to dominant and recessive epistasis. It was postulated that the the populations may have had segregation distortion commonly found in interspecific populations, thus the previously described genotypes for cotyledon colour and albino plants were used to test the hypothesis of segregation distortion. Segregation of these traits were found to be similarly distorted to previously reported interspecific <i>L. culinaris x L. ervoides</i> populations supporting the hypothesis that continued segregation distortion was found in the introgression populations. Overall, it was found that resistance derived from <i>L. ervoides</i> accession L-01-827A is a highly effective source for the lentil breeding program, however the result suggest more than one backcross to <i>L. culinaris</i> be necessary to properly integrate the resistance genes to eventually obtain fully fertile, adapted lentil cultivars.

The rapid development of large-scale genomic sequencing has dramatically changed the field of genetics, in part through the development of comparative genomics. Fungal comparative genomics is particularly powerful given the large number of genomes currently available, their compact architecture, and their relative ease of genetic manipulation. Fungal comparative genomics was employed in this work to address two related questions. First, it was used along with computational thermodynamic methods to predict non-coding RNA (ncRNA) in Saccharomyces cerevisiae. Sets of positive and negative control genes were evaluated to determine the effect of window sizes and step sizes on the sensitivity of ncRNA identification. The approach was then applied to predict ncRNA genes on chromosome 6 of S. cerevisiae and S. bayanus. Northern blot analysis, rapid amplification of cDNA ends (RACE), and publicly available cDNA library data were used to test the predictions. Strong experimental evidence was accumulated for four new ncRNA genes. Potential structural elements in the 5' and 3' untranslated regions (UTRs) of six annotated protein-coding genes were also identified. This work shows that thermodynamic approaches, coupled with comparative genomics, are powerful tools for predicting structural ncRNA. Second, comparative genomic approaches were employed to identify a non-reciprocal transfer event from Cryptococcus neoformans var. grubii to var. neoformans ~2 million years ago involving a 14 gene (~40 kb) region. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. The introgression event likely occurred via an incomplete inter-varietal sexual cycle creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. These data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that while evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role. / Dissertation

To increase genetic diversity with elite upland cotton, introgression populations with wild species of cotton, Gossypium mustelinum and G. tomentosum, were created. To accomplish this objective, F1, F2, BC1F1, and BC1F2 generations were developed along with random mating populations (BC1rm1 and BC1rm2) and grown in a randomized complete block design with four replications in College Station, Texas during 2003 and 2004, and in Mexico during 2005 for G. mustelinum introgression populations. These generations were tested with microsatellite markers from chromosome 11 in order to measure the effects of selection and recombination. Later generations (BC2F1, BC2rm1, BC2F2, BC3F1, BC3rm1 and BC3F2) and composite generations were evaluated in a randomized complete block design with four replications during 2004 and 2005 for agronomic properties. Introgression barriers for G. mustelinum were found to include daylength sensitivity and hybrid breakdown, which was only apparent in Mexico. Backcross generations had improved fiber quality. Random mating populations did not have increased variance and means differed little from BC1F1 levels. Microsatellite markers showed decreased frequency of G. mustelinum alleles and decreasing heterozygosity, but no increase in map distances in random mating populations. Upper-half mean length and upper quartile length by weight were highly heritable, as measured with parent-offspring regression. Most other agronomic traits had moderate heritabilities. Composite generations were found to be favorable for selection and breeding. For G. tomentosum populations, hybrid breakdown was also a problem with low yields for F2 and BC1F2 generations, but day length sensitivity was not. Little or no increase in variance was found in random mating populations when compared to BC1F1 levels. G. tomentosum populations did not show improvements in fiber length as seen in G. mustelinum populations, but did have increased strength in BC1F1 and F1 generations over TM-1. Mapping distances increased in the random mating populations for G. tomentosum, and the frequency of alien alleles did not decrease in random mating populations. Generation means approached recurrent parental values for most traits within three backcrosses. Composite generations were found to be the most useful for breeding and selection.

No description available.

An inter-specific linkage map of a backcross (BC1) population derived from a cross between C. tinctorius and C. oxyacanthus was developed using primarily microsatellite markers. A composite map, which aligned the inter-specific (C. tinctorius x C. oxyacanthus) map with an intra-specific linkage map previously developed from an F2 population of C. tinctorius, was created to search for syntenic regions. Results indicate that despite low marker saturation, there is substantial colinearity between the two linkage maps, and one translocation or inversion event. Upon subsequent self-fertilization events, phenotypes of the inter-specific backcross population were characterized in both the field (BC1S2 generation) and growth chamber (BC1S2 and BC1S3 generations), and identified several lines of agronomic interest. Introgression analysis was performed (BC1S3 generation) to assess the level of integration of C. oxyacanthus DNA into the C. tinctorius genome, and results are suggestive of less inter-specific recombination than expected. / Plant Biology

No description available.

The allohexaploid bread wheat (Triticum aestivum L.), evolved through a recent polyploidization event between tetraploid Triticum turgidum L. (AABB) and diploid Aegilops tauschii Coss. (DD), ~8,000 years ago. Contribution of only a subpopulation of Ae. tauschii to hexaploid evolution, followed by domestication and extensive breeding with the objective of higher yield gain and strict end-use quality determining the market classes of wheat, have created a genetic bottleneck. Synthetic hexaploid wheat (SHW) lines are generated to restore the diversity and exploit the genetic resource in the primary gene pool of wheat. However, there are challenges with recovering the phenotypes observed in the parental background in the hexaploid bread wheat in pre-breeding programs. To understand and characterize the barriers in utilizing the progenitor genetic diversity, the transcriptome of four SHW lines and their corresponding tetraploid and diploid parents across ten tissues, totalling to 240 samples, was analysed. The comparison of expression bias of homoeologues present as >18,000 triads (1:1:1) between parental in-silico SHW-like scenarios and SHWs, indicated a large-scale suppression of D subgenome homoeoalleles in SHWs. Tissue-specificity was not observed in the homoeologues of a large proportion of the triads. The next largest fractions were triads where all homoeologues displayed the same tissue-specific expression followed by those where only one of the homoeologues was tissue-specific. Several SHW-tissues showed moderate relationship between tissue-specificity of the homoeologues and expression bias of the corresponding triad. The repression of the genes of the D subgenome was also validated in the differential expression analysis using the entire high-confidence gene set of hexaploid wheat. Qualitative analysis of the transcripts revealed all five splicing events with predominance of retained introns, and more differentially-spliced transcripts were associated with the D homoeoalleles in most SHW-tissue contexts. The introgression patterns of the SHW-C66 into the elite bread wheat cultivar Carberry was analysed using a BC1F5 population. Large introgression of SHW-C66 were found closer to centromeric regions while smaller fragments were present towards the ends of the chromosomes. Correspondingly, the majority of the chromosomes showed higher recombination rates away from the centromere. The donor allele frequency was higher than the expected 25% for BC1F5 population in multiple regions of the A and B subgenomes but not in the D subgenome. In comparison, a preliminary analysis using an elite wheat × elite wheat doubled haploid population showed no subgenome-level variation in recombination rates or donor allele frequencies. In this thesis work, both functional genomic and structural genomic investigations using a set of SHW parents and their derivative population with elite wheat cultivars have unearthed some key patterns that add to the collective knowledge needed to fully exploit genetic resources in broadening the genetic diversity in wheat improvement programs.

Maize, Zea mays L., is the largest cereal grain crop grown in United States. Its yield and grain quality are adversely impacted by diseases every year. Aspergillus ear rot, caused by the fungus Aspergillus flavus, received little interest until its carcinogenic secondary metabolites, aflatoxins, were discovered. The objectives of this study were to introgress the quantitative trait loci (QTL) 2.04 from Mp313E and 5.03 from Mp715 into two commercial inbred lines, MonF and MonM; and evaluate their near isogenic lines (NILs) and testcrosses for preharvest aflatoxin accumulation and secondary agronomic traits. Marker assisted selection to create NILs and the testcross production was conducted by Bayer Company between 2015 and 2018. Field trials were conducted in summer 2019 as randomized complete block trials at three locations. The entry list of inbred trials included two donor parents (DP), two recurrent parents (RP), and their 58 NILs, and that of hybrid trials included 114 NIL testcrosses and 8 parental testcrosses. The top ear of each plant in every plot was inoculated with a 3.4 ml of A.flavus conidial suspension 13 days after mid-silk. All the inoculated ears were harvested at maturity, dried, machine shelled, ground, and aflatoxin concentration was determined by plot. Separate hybrid yield trials were conducted in four locations to measure the grain yield including an additional commercial check. Data on aflatoxin and other secondary traits was analyzed using SAS software. Overall, MonF NILs improved significantly more than MonM NILs in terms of their resistance to aflatoxin accumulation with the introgression of QTL 2.04 from Mp313E, but there were no differences with the introgression of QTL 5.03 from Mp715. Overall, Mp313E NILs improved more than Mp715 NILs when the recurrent parent was MonF, but the response was opposite when the recurrent parent was MonM. Compared to their respective recurrent parents, there were at least two NILs from each of the three out of four RP x DP crosses that significantly improved their resistance to aflatoxin accumulation with a minimal loss of their agronomic performance and testcross grain yields. These NILs could be considered as parents in future introgression projects.